Mean Relative Abundance Research Articles

Evaluation of temporary seasonal variation of heavy metals and their potential ecological risk in Nzhelele River, South Africa

AbstractSurface water is often used as alternative source of drinking water in many regions of the world where the potable water supply is erratic or not present. The concentration of heavy metals was assessed using an Inductively Coupled Plasma Optical Emission Spectrometer (ICP-OES). The impact of temporary seasonal variation on the contamination level was also assessed. Contamination factor (CF) and Hakanson’s potential ecological risk (Erand RI) indices were used to evaluate the toxicity levels of the metals in the sediments of the river. Higher concentrations of Fe, Mn, Pb, Cu and Zn were determined in the dry season in the river water whereas in the sediments higher levels were recorded for Al, Fe, Cd, Cr, Cu and Zn in the wet season. The average CF values for all the metals showed a low contamination level in the sediment, except for Cu and Cd which had moderate and considerable contamination levels, respectively. Similarly, Cu showed a moderate ecological risk level (Er= 62.90) only in March 2014, for other months Cu and the other metals investigated had Ervalues < 40 which implies low ecological risk. The mean relative abundance of heavy metals in the sediments follows the trend Al>Fe>Mn>u>Zn>Cr>Pb>Cd.

Successful Response to Microbiota-Based Drug RBX2660 in Patients with Recurrent Clostridium Difficile Infection is Associated with More Pronounced Alterations in Microbiome Profile

BackgroundRecurrent Clostridium difficile infections (rCDI) are associated with decreased diversity and altered intestinal microbiome compared with healthy patients. RBX2660, a standardized microbiota-based drug, is designed to restore microbiome diversity and composition in patients’. The effect of RBX2660 on rCDI patient microbiomes was evaluated by comparing pre- and post-treatment samples from PUNCH CD 2—a randomized, double-blind, placebo-controlled study.MethodsrCDIsubjects were randomized to receive blinded treatments of 2 doses of RBX2660 (Group A), 2 doses of placebo (Group B), or 1 dose each of RBX2660 and placebo (Group C), by enema 7 days apart. Subjects submitted stool samples at baseline, day 7, 30, and 60 after treatment. Stool samples from responders to RBX2660 treatment per protocol defined as the absence of CDI for 8 weeks after treatment were compared with non-responders.Relative taxonomic abundances at the class level were determined using 16s rRNA sequencing analysis for 94 stool samples from 45 patients in Groups A and C. Relative abundance data were grouped longitudinally using Bray-Curtis dissimilarity index. Analyses were performed based on the Dirichlet-Multinomial distribution to compare group mean relative taxonomic abundances; Simpson and Shannon diversity indices were compared among groups longitudinally.ResultsBaseline patient microbiomes were similar across response groups. RBX2660 treatment shifted the relative microbiome densities with taxa-specific increase in Bacteroidia, Clostridia, and decrease in Gamma-proteobacteria abundance. A larger shift from baseline microbiome was seen in responders to RBX2600 compared with non-responders (Figure 1). Microbiome changes in responders were durable to 60 days. RBX2660 treatment increased Shannon and Simpson diversity at 7 days post-treatment in responders but not in non-responders (P < 0.05).ConclusionRBX2660 treatment shifts patient intestinal microbiomes with greater alterations seen in those with a successful clinical outcome.Funded by Rebiotix Inc., Roseville, MN.Figure 1Responders to RBX2660 have a greater change in taxa abundance from baseline relative to non-responders at 30 days. Dirichlet-Multinomial parameter pi presented as mean (95% CI).Disclosures S. Khanna, Rebiotix, Inc.: Scientific Advisor, Consulting fee; K. Blount, Rebiotix, Inc.: Employee, Salary; C. Jones, Rebiotix, Inc.: Employee, Salary; B. Shannon, Rebiotix, Inc.: Research Contractor, Consulting fee; S. Carter, Rebiotix, Inc.: Research Contractor, Consulting fee

Oxidation of sitosterol and campesterol in foods upon cooking with liquid margarines without and with added plant sterol esters

Plant sterol (PS) oxidation products (POP) derived from sitosterol and campesterol were measured in 15 foods cooked with liquid margarine without (control) and with added 7.5% PS. POP were analyzed using a GC–MS method. PS liquid vs. control margarine resulted in a higher median POP content per food portion (1.35mg, range 0.08–13.20mg versus 0.23mg, 0.06–0.90mg), a lower PS oxidation rate (0.63 vs. 1.29%) and lower oxidation susceptibility of sitosterol vs. campesterol. POP formation was highest in shallow-fried potatoes with PS liquid margarine (64.44mg per portion food plus residual fat). Mean relative abundances of epoxy-, 7-keto-, 7-hydroxy- and triol-PS derived from sitosterol and campesterol were 40.0, 34.4, 21.5 and 4.0% with control vs. 44.1, 23.8, 29.6 and 2.4% with PS liquid margarine. In conclusion, PS liquid margarine increased POP content in foods with a POP profile characterized by a higher ratio of epoxy- to 7-keto-derivatives.

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment

BackgroundThe urinary microbiota is similarly complex as the vaginal and penile microbiota, yet its role as a reservoir for pathogens and for recurrent polymicrobial biofilm diseases like bacterial vaginosis (BV) is not clear.ResultsHere, we analysed the urinary microbiota of healthy men and women and compared it with that of women during BV and after antibiotic treatment using next-generation sequencing of the 16S rRNA gene V1-V2 regions. Eight different community types, so called urotypes (UT), were identified in healthy humans, all of which were shared between men and women, except UT 7, dominated in relative abundance by Lactobacillus crispatus, which was found in healthy women only. Orally applied metronidazole significantly reduced Shannon diversity and the mean relative abundance of Gardnerella vaginalis, Atopobium vaginae, and Sneathia amnii, while L. iners increased to levels twofold higher than those found in healthy women. Although individual urine microbial profiles strongly responded to the antibiotic, the healthy community could not be restored. The correlation between urinary and vaginal fluid microbiota was generally weak and depending on UT and BV status. It was highest in UT 1 in acute BV (59% of samples), but after metronidazole treatment, only 3 out of 35 women showed a significant correlation between their urinary and vaginal microbiota composition.ConclusionsUrethra and bladder thus harbor microbial communities distinct from the vagina. The high abundance of BV related species in the urine of both men and women suggests that urine may act as a reservoir of pathogens and contribute to recurrence.Trial registrationClinicalTrials.gov, NCT02687789

Production of Cow’s Milk Free from Beta-Casein A1 and Its Application in the Manufacturing of Specialized Foods for Early Infant Nutrition

Beta-casein (BC) is frequently expressed as BC A2 and BC A1 in cow’s milk. Gastrointestinal digestion of BC A1 results in the release of the opioid peptide beta-casomorphin 7 (BCM7) which is less likely to occur from BC A2. This work was aimed to produce milk containing BC A2 with no BC A1 (BC A2 milk) using genetically selected CSN2 A2A2 Jersey cows. Additionally, we aimed to develop an infant formula (IF) suitable for healthy full-term infants during the first six months of life based on BC A2 milk. The concentration of BCM7 released from BC A2 IF, from commercially available IFs as well as from human milk and raw cow’s milk was evaluated after simulated gastrointestinal digestion (SGID). BC A2 IF presented the lowest mean relative abundance of BC A1 (IF 1 = 0.136 ± 0.010), compared with three commercially available IFs (IF 2 = 0.597 ± 0.020; IF 3 = 0.441 ± 0.014; IF 4 = 0.503 ± 0.011). Accordingly, SGID of whole casein fraction from BC A2 IF resulted in a significantly lower release of BCM7 (IF 1 = 0.860 ± 0.014 µg/100 mL) compared to commercially available IFs (IF 2 = 2.625 ± 0.042 µg/100 mL; IF 3 = 1.693 ± 0.012 µg/100 mL; IF 4 = 1.962 ± 0.067 µg/100 mL). Nevertheless, BCM7 levels from BC A2 IF were significantly higher than those found in SGID hydrolysates of BC A2 raw milk (0.742 ± 0.008 µg/100 mL). Interestingly, results showed that BCM7 was also present in human milk in significantly lower amounts (0.697 ± 0.007 µg/100 mL) than those observed in IF 1 and BC A2 milk. This work demonstrates that using BC A2 milk in IF formulation significantly reduces BCM7 formation during SGID. Clinical implications of BC A2 IF on early infant health and development need further investigations.

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries.

Dental caries is the most prevalent disease in humans globally. Efforts to control it have been invigorated by an increasing knowledge of the oral microbiome composition. This study aimed to evaluate the bacterial diversity in occlusal biofilms and its relationship with clinical surface diagnosis and dietary habits. Anamneses were recorded from thirteen 12-year-old children. Biofilm samples collected from occlusal surfaces of 46 permanent second molars were analyzed by 16S rRNA amplicon sequencing combined with the BLASTN-based search algorithm for species identification. The overall mean decayed, missing and filled surfaces modified index [DMFSm Index, including active white spot lesions (AWSL)] value was 8.77±7.47. Biofilm communities were highly polymicrobial collectively, representing 10 bacterial phyla, 25 classes, 29 orders, 58 families, 107 genera, 723 species. Streptococcus sp_Oral_Taxon_065, Corynebacterium matruchotii, Actinomyces viscosus, Actinomyces sp_Oral_Taxon_175, Actinomyces sp_Oral_Taxon_178, Actinomyces sp_Oral_Taxon_877, Prevotella nigrescens, Dialister micraerophilus, Eubacterium_XI G 1 infirmum were more abundant among surfaces with AWSL, and Streptococcus gordonii, Streptococcus sp._Oral_Taxon_058, Enterobacter sp._str._638 Streptococcus australis, Yersinia mollaretii, Enterobacter cloacae, Streptococcus sp._Oral_Taxon_71, Streptococcus sp._Oral_Taxon_F11, Centipeda sp._Oral_Taxon_D18 were more abundant among sound surfaces. Streptococcus mutans was detected on all surfaces in all patients, while Streptococcus sobrinus was detected only in three patients (mean relative abundances 7.1% and 0.6%, respectively). Neither species differentiated healthy from diseased sites. Diets of nine of the subjects were scored as high in fermentable carbohydrates (≧2X/day between meals). A direct association between relative abundances of bacteria and carbohydrate consumption was observed among 18 species. High consumption of fermentable carbohydrates and sound surfaces were associated with a reduction in bacterial diversity. PCoA plots displayed differences in bacterial community profiles between sound and diseased surfaces. Our study showed that, in addition to mutans streptococci, other species may be associated with the initiation of dental caries on occlusal surfaces, and that biofilm diversity of tooth surfaces is influenced by carbohydrate consumption and a surface’s health status.

Mammalian species abundance across a gradient of tropical land-use intensity: A hierarchical multi-species modelling approach

Recent work in the tropics has advanced our understanding of the local impacts of land-use change on species richness. However, we still have a limited ability to make predictions about species abundances, especially in heterogeneous landscapes. Species abundances directly affect the functioning of an ecosystem and its conservation value. We applied a hierarchical model to camera- and live-trapping data from a region in Borneo, and estimated the relative abundance (controlling for imperfect detection) of 57 terrestrial mammal species, as a function of either categorical or continuous metrics of land-use change. We found that mean relative abundance increased (by 28%) from old-growth to logged forest, but declined substantially (by 47%) in oil palm plantations compared to forest. Abundance responses to above-ground live tree biomass (a continuous measure of local logging intensity) were negative overall, whilst they were strongly positive for landscape forest cover. From old-growth to logged forest, small mammals increased in their relative abundance proportionately much more than large mammals (169% compared to 13%). Similarly, omnivores and insectivores increased more than other trophic guilds (carnivores, herbivores and frugivores). From forest to oil palm, species of high conservation concern fared especially poorly (declining by 84%). Invasive species relative abundance consistently increased along the gradient of land-use intensity. Changes in relative abundance across nine functional effects groups based on diet were minimal from old-growth to logged forest, but in oil palm only the vertebrate predation function was maintained. Our results show that, in the absence of hunting, even the most intensively logged forests can conserve the abundance and functional effects of mammals. Recent pledges made by companies to support the protection of High Carbon Stock logged forest could therefore yield substantial conservation benefits. Within oil palm, our results support the view that “wildlife-friendly” practices offer a low potential for reducing biodiversity impacts.

Alien vs. predator: bacterial challenge alters coral microbiomes unless controlled by Halobacteriovorax predators.

Coral microbiomes are known to play important roles in organismal health, response to environmental stress, and resistance to disease. The coral microbiome contains diverse assemblages of resident bacteria, ranging from defensive and metabolic symbionts to opportunistic bacteria that may turn harmful in compromised hosts. However, little is known about how these bacterial interactions influence the mechanism and controls of overall structure, stability, and function of the microbiome. We sought to test how coral microbiome dynamics were affected by interactions between two bacteria: Vibrio coralliilyticus, a known temperature-dependent pathogen of some corals, and Halobacteriovorax, a unique bacterial predator of Vibrio and other gram-negative bacteria. We challenged reef-building coral with V. coralliilyticus in the presence or absence of Halobacteriovorax predators, and monitored microbial community dynamics with 16S rRNA gene profiling time-series. Vibrio coralliilyticus inoculation increased the mean relative abundance of Vibrios by greater than 35% from the 4 to 8 hour time point, but not in the 24 & 32 hour time points. However, strong secondary effects of the Vibrio challenge were also observed for the rest of the microbiome such as increased richness (observed species), and reduced stability (increased beta-diversity). Moreover, after the transient increase in Vibrios, two lineages of bacteria (Rhodobacterales and Cytophagales) increased in coral tissues, suggesting that V. coralliilyticus challenge opens niche space for these known opportunists. Rhodobacterales increased from 6.99% (±0.05 SEM) to a maximum mean relative abundance of 48.75% (±0.14 SEM) in the final time point and Cytophagales from <0.001% to 3.656%. Halobacteriovorax predators are commonly present at low-abundance on coral surfaces. Based on the keystone role of predators in many ecosystems, we hypothesized that Halobacteriovorax predators might help protect corals by consuming foreign or “alien” gram negative bacteria. Halobacteriovorax inoculation also altered the microbiome but to a lesser degree than V. coralliilyticus, and Halobacteriovorax were never detected after inoculation. Simultaneous challenge with both V. coralliilyticus and predatory Halobacteriovorax eliminated the increase in V. coralliilyticus, ameliorated changes to the rest of the coral microbiome, and prevented the secondary blooms of opportunistic Rhodobacterales and Cytophagales seen in the V. coralliilyticus challenge. These data suggest that, under certain circumstances, host-associated bacterial predators may mitigate the ability of other bacteria to destabilize the microbiome.

Bacterial Composition and Diversity in Breast Milk Samples from Mothers Living in Taiwan and Mainland China.

Human breast milk is widely recognized as the best source of nutrients for healthy growth and development of infants; it contains a diverse microbiota. Here, we characterized the diversity of the microbiota in the breast milk of East Asian women and assessed whether delivery mode influenced the microbiota in the milk of healthy breast-feeding mothers. We profiled the microbiota in breast milk samples collected from 133 healthy mothers in Taiwan and in six regions of mainland China (Central, East, North, Northeast, South, and Southwest China) by using 16S rRNA pyrosequencing. Lactation stage (months postpartum when the milk sample was collected) and maternal body mass index did not influence the breast milk microbiota. Bacterial composition at the family level differed significantly among samples from the seven geographical regions. The five most predominant bacterial families were Streptococcaceae (mean relative abundance: 24.4%), Pseudomonadaceae (14.0%), Staphylococcaceae (12.2%), Lactobacillaceae (6.2%), and Oxalobacteraceae (4.8%). The microbial profiles were classified into three clusters, driven by Staphylococcaceae (abundance in Cluster 1: 42.1%), Streptococcaceae (Cluster 2: 48.5%), or Pseudomonadaceae (Cluster 3: 26.5%). Microbial network analysis at the genus level revealed that the abundances of the Gram-positive Staphylococcus, Streptococcus, and Rothia were negatively correlated with those of the Gram-negative Acinetobacter, Bacteroides, Halomonas, Herbaspirillum, and Pseudomonas. Milk from mothers who had undergone Caesarian section (C-section group) had a significantly higher abundance of Lactobacillus (P < 0.05) and a higher number of unique unclassified operational taxonomic units (OTUs) (P < 0.001) than that from mothers who had undergone vaginal delivery (vaginal group). These findings revealed that (i) geographic differences in the microbial profiles were found in breast milk from mothers living in Taiwan and mainland China, (ii) the predominant bacterial families Streptococcaceae, Staphylococcaceae, and Pseudomonadaceae were key components for forming three respective clusters, and (iii) a significantly greater number of unique OTUs was found in the breast milk from mothers who had undergone C-section than from those who had delivered vaginally.

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis.

Increasing attention is being focused on evaluating the salivary microbiota as a promising method for monitoring oral health; however, its bacterial composition greatly differs from that of dental plaque microbiota, which is a dominant etiologic factor of oral diseases. This study evaluated the relative abundance of subgingival plaque-specific bacteria in the salivary microbiota and examined a relationship between the abundance and severity of periodontal condition in patients with periodontitis. Four samples (subgingival and supragingival plaques, saliva, and tongue coating) per each subject were collected from 14 patients with a broad range of severity of periodontitis before periodontal therapy. The bacterial composition was analyzed by 16S rRNA gene amplicon sequencing using Ion PGM. Of the 66 species-level operational taxonomic units (OTUs) representing the mean relative abundance of ≥ 1% in any of the four niches, 12 OTUs corresponding to known periodontal pathogens, including Porphyromonas gingivalis, were characteristically predominant in the subgingival plaque and constituted 37.3 ± 22.9% of the microbiota. The total relative abundance of these OTUs occupied only 1.6 ± 1.2% of the salivary microbiota, but significantly correlated with the percentage of diseased sites (periodontal pocket depth ≥ 4 mm; r = 0.78, P < 0.001), in addition to the abundance of subgingival plaque microbiota (r = 0.61, P = 0.02). After periodontal therapy, the total relative abundance of these 12 OTUs was evaluated as well as before periodontal therapy and reductions of the abundance through periodontal therapy were strongly correlated in saliva and subgingival plaque (r = 0.81, P < 0.001). Based on these results, salivary microbiota might be a promising target for the evaluation of subgingival plaque-derived bacteria representing the present condition of periodontal health.

Increased risk of pneumonia in residents living near poultry farms: does the upper respiratory tract microbiota play a role?

BackgroundAir pollution has been shown to increase the susceptibility to community-acquired pneumonia (CAP). Previously, we observed an increased incidence of CAP in adults living within 1 km from poultry farms, potentially related to particulate matter and endotoxin emissions. We aim to confirm the increased risk of CAP near poultry farms by refined spatial analyses, and we hypothesize that the oropharyngeal microbiota composition in CAP patients may be associated with residential proximity to poultry farms.MethodsA spatial kernel model was used to analyze the association between proximity to poultry farms and CAP diagnosis, obtained from electronic medical records of 92,548 GP patients. The oropharyngeal microbiota composition was determined in 126 hospitalized CAP patients using 16S-rRNA-based sequencing, and analyzed in relation to residential proximity to poultry farms.ResultsKernel analysis confirmed a significantly increased risk of CAP when living near poultry farms, suggesting an excess risk up to 1.15 km, followed by a sharp decline. Overall, the oropharyngeal microbiota composition differed borderline significantly between patients living <1 km and ≥1 km from poultry farms (PERMANOVA p = 0.075). Results suggested a higher abundance of Streptococcus pneumoniae (mean relative abundance 34.9% vs. 22.5%, p = 0.058) in patients living near poultry farms, which was verified by unsupervised clustering analysis, showing overrepresentation of a S. pneumoniae cluster near poultry farms (p = 0.049).ConclusionLiving near poultry farms is associated with an 11% increased risk of CAP, possibly resulting from changes in the upper respiratory tract microbiota composition in susceptible individuals. The abundance of S. pneumoniae near farms needs to be replicated in larger, independent studies.

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons

BackgroundThe vaginal microbiome is an important site of bacterial-mammalian symbiosis. This symbiosis is currently best characterized for humans, where lactobacilli dominate the microbial community and may help defend women against infectious disease. However, lactobacilli do not dominate the vaginal microbiota of any other mammal studied to date, raising key questions about the forces that shape the vaginal microbiome in non-human mammals.ResultsWe used Illumina sequencing of the bacterial 16S rRNA gene to investigate variation in the taxonomic composition of the vaginal microbiota in 48 baboons (Papio cynocephalus), members of a well-studied wild population in Kenya. Similar to prior studies, we found that the baboon vaginal microbiota was not dominated by lactobacilli. Despite this difference, and similar to humans, reproductive state was the dominant predictor of baboon vaginal microbiota, with pregnancy, postpartum amenorrhea, and ovarian cycling explaining 18% of the variance in community composition. Furthermore, among cycling females, a striking 39% of variance in community composition was explained by ovarian cycle phase, with an especially distinctive microbial community around ovulation. Periovulatory females exhibited the highest relative abundance of lactic acid-producing bacteria compared to any other phase, with a mean relative abundance of 44%. To a lesser extent, sexual behavior, especially a history of shared sexual partners, also predicted vaginal microbial similarity between baboons.ConclusionsDespite striking differences in their dominant microbes, both human and baboon vaginal microbiota exhibit profound changes in composition in response to reproductive state, ovarian cycle phase, and sexual behavior. We found major shifts in composition during ovulation, which may have implications for disease risk and conception success. These findings highlight the need for future studies to account for fine-scale differences in reproductive state, particularly differences between the various phases of the ovarian cycle. Overall, our work contributes to an emerging understanding of the forces that explain intra- and inter-individual variation in the mammalian vaginal microbiome, with particular emphasis on its role in host health and disease risk.

Diversity and Abundance of Avian Species of Owena Multipurpose Dam, Ondo State, Southwest, Nigeria

The use of wetlands and their resources is widespread among many diverse bird taxa of the world. The diversity and abundance of avian species in Owena Multipurpose dam was assessed out between January and June, 2016 to provide baseline information of the birds in this area. The line transects method with lengths ranging from 350 m-1000 m was adopted for the survey. Birds recorded were categorized into order, family, species, migratory status and feeding guild. Relative abundance of bird species and diversity indices were determined. Significance in mean bird density in the two seasons was determined using T-test while One-Way ANOVA was used to test for significance in bird diversity indices. A total of 35 bird species belonging to 20 families and 10 orders were recorded in the study area. The common species includes Ardea alba, Vanellus spinosus, Ardea cinerea, Phalacrocorax carbo, Milvus migrans, Ardeola ralloides, Actophilornis africanus, Microcarbo africanus, and Bubulcus ibis. All the bird species recorded were in the Least Concern (LC) category. The bird species were categorized into seven feeding guilds. The granivores, insectivores and canivores were more in abundance than the nectarivores and frugivores. The order Passeriformes had the highest families (9) and species (17), followed by Pelecaniformes and Charadriiformes with 2 families each, 4 and 2 species respectively while others had one family each. The total mean number of bird was 428 ± 5.75/ observation. Lagonosticta sanguinodorsalis had the highest mean number (156.4/ observation) and relative abundance of 36.54% while Ardae cinerea and Phalacrocorax carbo had the lowest mean number (0.2/ observation) and relative abundance of 0.05% each. Transect 1 had the highest Shannon diversity index (Hl=1.664), while transect 3 had the least (1.168). All the transects had similar species evenness index except for transect 4. The findings can be attributed to the heterogeneity of the habitat resulting from alteration of the ecosystem through the construction of the dam. In conclusion, the Owena dam construction has both negative and positive impacts on avian species composition and abundance. The management programme of the Owena dam should incorporate avian conservation in the area.

Porphyromonas gingivalis is the most abundant species detected in coronary and femoral arteries

ABSTRACTAn association between oral bacteria and atherosclerosis has been postulated. A limited number of studies have used 16S RNA gene sequencing-based metagenomics approaches to identify bacteria at the species level from atherosclerotic plaques in arterial walls. The objective of this study was to establish detailed oral microbiome profiles, at both genus and species level, of clinically healthy coronary and femoral artery tissues from patients with atherosclerosis. Tissue specimens were taken from clinically non-atherosclerotic areas of coronary or femoral arteries used for attachment of bypass grafts in 42 patients with atherosclerotic cardiovascular disease. Bacterial DNA was sequenced using the MiSeq platform, and sequence reads were screened in silico for nearly 600 oral species using the HOMINGS ProbeSeq species identification program. The number of sequence reads matched to species or genera were used for statistical analyses. A total of 230 and 118 species were detected in coronary and femoral arteries, respectively. Unidentified species detected by genus-specific probes consisted of 45 and 30 genera in coronary and in femoral artery tissues, respectively. Overall, 245 species belonging to 95 genera were detected in coronary and femoral arteries combined. The most abundant species were Porphyromonas gingivalis, Enterococcus faecalis, and Finegoldia magna based on species probes. Porphyromonas, Escherichia, Staphylococcus, Pseudomonas, and Streptococcus genera represented 88.5% mean relative abundance based on combined species and genus probe detections. Porphyromonas was significantly more abundant than Escherichia (i.e. 46.8% vs. 19.3%; p = 0.0005). This study provides insight into the presence and types of oral microbiome bacterial species found in clinically non-atherosclerotic arteries.

Performance of hymenopteran insects as pollinators of pumpkin in Meghalaya

Pumpkin is a major cultivated crop particularly in north eastern states of India that depends on insects for the pollination, as the pollens of these plants are large sized and sticky. In the present study, field and lab experiments were conducted to determine the efficiency of the pollinators of pumpkin based on their diversity, relativeabundance and foraging activity. Total four hymenopteran insect pollinators were observed in field viz., bumble bee, little honey bee, Indian honey bee and Digger bee. On the basis of abundance and relative abundance bumble bee was identified as most abundant pollinator of pumpkin with 69.69 per cent mean relative abundance as other pollinators mean relative abundance was less than 25 per cent and it was only 3.49 per cent for Indian honey bee. Foraging speed and foraging rate of bumble bee was 7.13 sec/flower and foraging rate was 3.80 flower/minute. To ensure the efficient pollinator of pumpkin flower, pollen carrying capacity, pollen deposition and percent deposition of viable pollen was studied for all the pollinators in field and laboratory condition. The pollen carrying capacity of pollinators ranged from more than 7 mg to 1 mg. It was highest for bumble bee which was 7.33 mg followed by little honey bee (6.66 mg) and least pollen carrying capacity was observed in Digger bee (1.67 mg). Pollen depositions by pollinators on stigma in a single visit was again highest for bumble bee (565 pollen grains) with maximum number of viable pollen deposition 224.33 pollen grains out of which 39.7 per cent pollen was viable. So on the basis of above result it can be concluded that bumble bee was the most abundant and most efficient pollinator of pumpkin.

Pre- and post-weaning diet alters the faecal metagenome in the cat with differences in vitamin and carbohydrate metabolism gene abundances.

Dietary format, and its role in pet nutrition, is of interest to pet food manufacturers and pet owners alike. The aim of the present study was to investigate the effects of pre- and post-weaning diets (kibbled or canned) on the composition and function of faecal microbiota in the domestic cat by shotgun metagenomic sequencing and gene taxonomic and functional assignment using MG-RAST. Post-weaning diet had a dramatic effect on community composition; 147 of the 195 bacterial species identified had significantly different mean relative abundances between kittens fed kibbled and canned diets. The kittens fed kibbled diets had relatively higher abundances of Lactobacillus (>100-fold), Bifidobacterium (>100-fold), and Collinsella (>9-fold) than kittens fed canned diets. There were relatively few differences in the predicted microbiome functions associated with the pre-weaning diet. Post-weaning diet affected the abundance of functional gene groups. Genes involved in vitamin biosynthesis, metabolism, and transport, were significantly enriched in the metagenomes of kittens fed the canned diet. The impact of post-weaning diet on the metagenome in terms of vitamin biosynthesis functions suggests that modulation of the microbiome function through diet may be an important avenue for improving the nutrition of companion animals.

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

Fanconi anemia (FA) is a rare genetic disease characterized by chromosomal instability and impaired DNA damage repair. FA patients develop oral squamous cell carcinoma (OSCC) earlier and more frequently than the general population, especially after hematopoietic stem cell transplantation (HSCT). Although evidence of an etiological role of the local microbiome and carcinogenesis has been mounting, no information exists regarding the oral microbiome of FA patients. The aim of this study was to explore the salivary microbiome of 61 FA patients regarding their oral health status and OSCC risk factors. After answering a questionnaire and receiving clinical examination, saliva samples were collected and analyzed using 16S rRNA sequencing of the V3-V4 hypervariable region. The microbial profiles associated with medical and clinical parameters were analyzed using general linear models. Patients were young (mean age, 22 y) and most had received HSCT (n = 53). The most abundant phyla were Firmicutes [mean relative abundance (SD), 42.1% (10.1%)] and Bacteroidetes [(25.4% (11.4%)]. A history of graft-versus-host disease (GVHD) (n = 27) was associated with higher proportions of Firmicutes (43.8% × 38.5%, P = 0.05). High levels of gingival bleeding were associated with the genera Prevotella (22.25% × 20%), Streptococcus (19.83% × 17.61%), Porphyromonas (3.63% × 1.42%, P = 0.03), Treponema (1.02% × 0.28%, P = 0.009), Parvimonas (0.28% × 0.07%, P = 0.02) and Dialister (0.27% × 0.10%, P = 0.04). Finally, participants transplanted over 11 y ago showed the highest levels of Streptococcus (18.4%), Haemophilus (12.7%) and Neisseria (6.8%). In conclusion, FA patients that showed poor oral hygiene harbored higher proportions of the genera of bacteria compatible with gingival disease. Specific microbial differences were associated with a history of oral GVHD and a history of oral mucositis.

Identification of Anion Channels Responsible for Fluoride Resistance in Oral Streptococci.

Recently, it has been reported that eriC and crcB are involved in bacterial fluoride resistance. However, the fluoride-resistance mechanism in oral streptococci remains unclear. BLAST studies showed that two types of eriCs (eriC1 and eriC2) and two types of crcBs (crcB1 and crcB2) are present across 18 oral streptococci, which were identified in ≥ 10% of 166 orally healthy subjects with ≥ 0.01% of the mean relative abundance. They were divided into three groups based on the distribution of these four genes: group I, only eriC1; group II, eriC1 and eriC2; and group III, eriC2, crcB1, and crcB2. Group I consisted of Streptococcus mutans, in which one of the two eriC1s predominantly affected fluoride resistance. Group II consisted of eight species, and eriC1 was responsible for fluoride resistance, but eriC2 was not, in Streptococcus anginosus as a representative species. Group III consisted of nine species, and both crcB1 and crcB2 were crucial for fluoride resistance, but eriC2 was not, in Streptococcus sanguinis as a representative species. Based on these results, either EriC1 or CrcBs play a role in fluoride resistance in oral streptococci. Complementation between S. mutans EriC1 and S. sanguinis CrcB1/CrcB2 was confirmed in both S. mutans and S. sanguinis. However, neither transfer of S. sanguinis CrcB1/CrcB2 into wild-type S. mutans nor S. mutans EriC1 into wild-type S. sanguinis increased the fluoride resistance of the wild-type strain. Co-existence of different F− channels (EriC and CrcB) did not cause the additive effect on fluoride resistance in oral Streptococcus species.

Identification of the Bacterial Reservoirs for the Middle Ear Using Phylogenic Analysis

The adenoid pad has long been considered a reservoir for bacteria in the pathogenesis of otitis media with effusion (OME). However, bacteria more reminiscent of external auditory canal (EAC) commensals are often demonstrated within middle ear aspirates. To compare the microbiota of the EAC, the middle ear with OME, and the adenoid pad to further clarify the true source of middle ear bacteria. Middle ear fluid (MEF) aspirates and EAC lavages were collected from 18 children with OME undergoing ventilation tube insertion from June 1, 2014, to August 31, 2015, at Women and Children's Hospital, Adelaide, Australia. Adenoid pad and MEF samples were included from a previous study. Samples were analyzed using sequencing of the 16S ribosomal RNA gene. Previously collected microbiota data from the adenoid pad were collated for analysis. Mean relative abundance of top bacterial genera for the MEF, EAC, and adenoid pad samples. Eighteen pediatric patients with chronic OME (6 female; 12 male; mean [SD] age, 48 [36] months) were recruited prospectively, with 34 paired MEF and EAC samples. The MEF microbiota (mean relative abundance [SD]) consisted of Alloiococcus otitidis (37.5% [40.0%]), Haemophilus (14.4% [29.1%]), Moraxella (10.0% [26.4%]), Staphylococcus (8.2% [21.9%]), and Streptococcus (3.8% [13.1%]). The mean relative abundance (SD) microbiota of the EAC demonstrated a sparsity of classic otopathogens, including Haemophilus (0.3% [0.8%]), Moraxella (0.3% [0.7%]), and Streptococcus (0.2% [0.6%]), but had a high abundance of Alloiococcus (58.0% [44.1%]), Staphylococcus (20.8% [34.0%]), and Pseudomonas (3.2% [17.1%]). In contrast, based on previously collected data, the microbiota of the adenoid pad showed a high abundance of the classic otopathogens with a sparsity of EAC genera for Alloiococcus (0.1% vs 28.9%, respectively; P < .001), Haemophilus (25.2% vs 18.2%, respectively; P = .002), Staphylococcus (0.2% vs 10.8%, respectively; P = .02), Streptococcus (12.7% vs 4.2%, respectively; P < .001), and Pseudomonas (0 vs 2.1% respectively; P < .001). The microbiota of the MEF collected during 2 consecutive years were similar (Alloiococcus, 22.7% vs 37.5%; Haemophilus, 22.5% vs 14.0%; Staphylococcus, 10.9% vs 10.7%; Moraxella, 5.0% vs 9.7%; Corynebacteria, 6.2% vs 3.1%; Streptococcus, 4.8% vs 3.7%; and Pseudomonas, 1.1% vs 3.0%; P ≥ .05). The EAC and the nasopharynx could serve as reservoirs for microbiota of the middle ear. Furthermore, the microbiota of the middle ear with effusion appear to be relatively stable over time and between populations with OME.

Intestinal carriage of Extended Spectrum Beta-Lactamase producing E. coli in women with urinary tract infections, Cameroon.

During the last decade, the prevalence of the intestinal carriage of extended spectrum beta-lactamases - producing Escherichia coli (ESBL-E. coli) has continued to increase worldwide in the community, especially in developing countries. Hence, we undertook a study to determine the ESBL-E. coli fecal carriage rate and the associated risk factors in Cameroonian women. A total of 86 women suspected of community-acquired urinary tract infections (UTI) were included in 10 health structures from May 2011 to April 2012. After filling a questionnaire, they provided a stool sample that was plated on selective media for ESBL producing bacteria. The identification of strains was obtained with mass spectrometry and the antibiotic susceptibility by disk diffusion in agar media. The ESBL type was determined by PCR. The relative abundance of ESBL-E. coli was measured for positive samples. Eventually, the presence of antibiotics in stool was assessed. The carriage rate of ESBL-E. coli was 57/86 (66.3%). Phenotypic and molecular characterization showed that all ESBL-E. coli strains contained group 1 CTX-M enzymes. Multivariate analysis showed that ESBL-E. coli fecal carriage was associated with the presence of antibiotics in stools (p < 0.05). Although not significant, mean ESBL relative abundance tended to be higher in patients with antibiotic exposure. Our results show that the carriage of ESBL-E. coli fecal carriage in women with UTI suspicion from the Cameroonian community is extremely high and associated with recent antibiotic intake.